Welcome to #AGA2024!! Here we will share some bits, pieces, and anecdotes from this year’s presidential symposium! Our president Beth Shapiro put together a great list of speakers and we have many excellent poster presenters.
Day 3: AM Talks
Elinor Karlsson, Exploring the evolution of exceptional traits through comparative genomics in hundreds of mammals
Elinor is the director of the Vertebrate Genomics Group at the Broad Institute and a professor in Bioinformatics and Integrative Biology at the University of Massachusetts Medical School. Her work involves studying nonhuman animals in order to understand human genomes. She works on such cool projects as the Darwin’s Ark pet project(s) and broadly searches genomes to determine when, where, and how DNA mutates.
90% of the known disease-causing variants are located in the coding regions within genomes (exons). Since humans are relatively recently diverged species, tracing the origin of genome mutations is much more informative when you have information from many other species with much more ancient lineages.- As part of the Zoonomia Project, genomes from 240 placental mammals were sequenced, aligned, and mutations traced.
- Findings include that ~11% of the human genome is evolutionarily constrained, there are 4500+ ultra-conserved regions in the vertebrate genome
- Other uses for this data include investigating longevity (such as why the greater mouse-eared bats don’t seem to age like other animals do), what genes are involved in the evolution of hibernation, and predicting active enhancer regions in order to analyze genes involved in changes in brain size.
- Next steps involve stepping from correlation to function/causation, which involves an animal-based common garden experiment using fibroblast cells
- An experiment compared camels (which can vary their body temperature from 37-42C and not be too perturbed) and other temperature-extreme species (such as hibernators) to other species that are not able to withstand such crazy changes in body temperature. They found drastic changes in cell physiology as well as gene expression changes across an entire suite of genes related to hibernation and heat tolerance conserved across species.
Joanna Kelley, Population genomics enables conservation
Joanna studies adaptations to extreme environments at UC Santa Cruz. Brown bears (aka Grizzly bears) have three main activity cycles: hibernation in the winter where they have a decreased metabolic rate, an active/normal phase where they roam around doing bear things, and a hyperphagic cycle where they consume as much as possible before hibernation (and lead to things like Fat Bear Week). However, brown bears are very prone to human-wildlife conflict.
- As brown bears have male-biased dispersal, investigating the Y chromosome (in brown bears, like humans, the males have a Y chromosome) may help provide further insight into why male bears are different (data is preliminary!)
- North American brown bears occupy only about half of their historic range due to climate change, habitat loss, and human-wildlife conflict
- In the lower 48 contiguous United States, this drops to only 3% of their historic range. This has led to a slightly contentious listing under the Endangered Species Act that has gone back and forth (aka Yoyo-ed) since the original listing in 1975.
- It’s imperative to work with managers to design studies that provide information that benefits the bears, managers, and the scientific community as a whole.
- This collaboration will use genomic data to determine the population structure of grizzly bears within management units or populations of interest. Genomics will improve upon the current use of microsatellites.
- Analyses are preliminary so we will not share more here (by request), but stay tuned for the full story!!
- The ultimate goal of this work is to develop a conservation SNP panel that allows managers to take a minION or similar portable sequencer to genotype bears out in the field and garner population information much faster than current data allows
- However, it is also key to link SNP data with the existing microsatellite data so that managers can still take advantage of the treasure trove of existing genotype data so that information is not lost.
Moi Exposito-Alonso, Rapid evolution across climates in a globally synchronized experiment of an annual herb
Moi is the Howard Hughes Medical Institute Freeman Hrabowski Scholar and Assistant Professor at UC Berkeley. His lab uses molecular tools to investigate the ecology of global change. Rapid adaptation has been investigated since Darwin’s time (and honestly probably before that, we just don’t have a reliable record of it) so he is investigating the questions: 1) Can populations rapidly evolve/adapt to new climates, and 2) Is there enough existing diversity to facilitate such adaptation?
- Arabidopsis thaliana is a well-documented model species that also has many, many natural populations spread across the globe and in many extreme environments.
- This led to a massive common garden partnership called GrENE-net that has sequenced over 70,000 individuals in over 30 locations internationally.
- Due to the breadth and scope of this data, reconstructing allele frequencies over time is possible, as well as observing many different phenotypes (the plants are many different colors!).
- Findings using allele frequency changes indicate the plants adapt at different rates (and different directions) across temperature gradients and a genome-wide association study (GWAS) of SNPs shows that alleles within genes are selected in different directions based on the temperature (some alleles increase in warmer temperatures and decrease in cooler temperatures).
- Can we use this kind of data to predict evolution? Past common garden studies imply strong local adaptation, but this data is most qualitative. This new data can now create quantitative evidence for local adaptation and then model climate change adaptation.
- Creating global predictions of genetic diversity (plants especially) is quite challenging. Using Arabidopsis as a proxy shows that genetic diversity follows a power law where genetic diversity varies in proportion to the area the species occupies, so genetic diversity will decrease in a (relatively) predictable way as species ranges shrink.
- this prediction was initially made using plant data but later validated using genomic data from other plants and animals
- What does this mean? With current habitat loss, we have already likely lost at least 10% of the genetic diversity across all species so biodiversity goals from the IUCN and similar entities should be adjusted accordingly.